We have crystallized and solved the structure of the catalytic domain of human PPM1A complexed with a cyclic phosphopeptide inhibitor that mimics the activation loop of p38 MAPK (1), one of the physiological substrates of PPM1A. We therefore have confirmed the suspected presence of a third metal ion in the active site of metazoan PPM phosphatases. Further biophysical and computational studies suggested that complex formation results in a more compact solution conformation through reduced conformational flexibility of the Flap subdomain. We also observed that the position of the substrate in the active site allows solvent access to the labile third metal-binding site. Enzyme kinetic studies with a phosphopeptide substrate provided evidence for a random-order, bi-substrate mechanism, with substantial interaction between the bound substrate and the labile metal ion. Our work has revealed the structural and thermodynamic basis of an innate mechanism regulating the activity of PPM phosphatases. 1. Debnath et al. (2018) A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity. J. Biol. Chem. 293, 7993-8008.